Lecture 7: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Logical Volume Management ("LVM") on linux looks like a complicated mess at first. The basics are not all that hard, and some features like mirroring, dynamic space management, snapshots for stable backups, mirroring, and over-provisioning via thin volumes can save a lot of time and effort.
전체목차: https://netpple.github.io/docs/make-container-without-docker/
클라우드 위에서 컨테이너에 가상 IP를 부여하고 이러한 가상 IP대역을 기반으로 컨테이너 간에 통신이 어떻게 가능한 것일까요?
동적으로 오버레이 네트워크를 구성해 봅니다.
지난 시간 가상IP 대역을 기반으로 서로 다른 물리노드 간의 통신을 가능하기 위하여 가상 디바이스를 생성하고 ARP cache와 Bridge FDB 정보를 입력해주고, vxlan 기반의 UDP encapsulation과 터널링을 통하여 가상디바이스의 L2정보를 목적지 노드로 전송하여 통신이 되는 것을 확인하였습니다.
이에 대한 내용을 바탕으로 가상네트워크를 추가하고 통신할 때 커널 이벤트(NETLINK)를 캐치하여 동적으로 arp, fdb 갱신처리하여 컨테이너 간에 통신이 가능하도록 구성해 봅니다.
Make container without_docker_6-overlay-network_1 Sam Kim
분산환경에서 컨테이너 간의 통신은 어떻게 이루어 지는 것일까요? 3,4편에서는 호스트 안에 가상네트워크를 만들어보았습니다. 6편에서는 이를 바탕으로 분산환경에서 호스트 간에 가상 네트워크로 통신이 가능하도록 만들어 봅니다. 이 방법은 실제 쿠버네티스 flannel 등의 CNI에서 사용하고 있는 vxlan 기반의 오버레이 네트워크 구성을 다룹니다.
[Open Infrastructure & Cloud Native Days Korea 2019]
커뮤니티 버전의 OpenStack 과 Ceph를 활용하여 대고객서비스를 구축한 사례를 공유합니다. 유연성을 확보한 기업용 클라우드 서비스 구축 사례와 높은 수준의 보안을 요구하는 거래소 서비스를 구축, 운영한 사례를 소개합니다. 또한 이 프로젝트에 사용된 기술 스택 및 장애 해결사례와 최적화 방안을 소개합니다. 오픈스택은 역시 오픈소스컨설팅입니다.
#openstack #ceph #openinfraday #cloudnative #opensourceconsulting
NovaProva, a new generation unit test framework for C programsGreg Banks
I wrote NovaProva because I was sick of writing unit tests using the venerable but clunky CUnit library. CUnit looked easy when I started writing unit tests but I soon discovered it's limitations and ended up screaming in frustration. Meanwhile over 18 months the Cyrus IMAP server project has gone from 0 unit tests to 461, of which 277 are written in C with CUnit. So that's a big itch!
Logical Volume Management ("LVM") on linux looks like a complicated mess at first. The basics are not all that hard, and some features like mirroring, dynamic space management, snapshots for stable backups, mirroring, and over-provisioning via thin volumes can save a lot of time and effort.
전체목차: https://netpple.github.io/docs/make-container-without-docker/
클라우드 위에서 컨테이너에 가상 IP를 부여하고 이러한 가상 IP대역을 기반으로 컨테이너 간에 통신이 어떻게 가능한 것일까요?
동적으로 오버레이 네트워크를 구성해 봅니다.
지난 시간 가상IP 대역을 기반으로 서로 다른 물리노드 간의 통신을 가능하기 위하여 가상 디바이스를 생성하고 ARP cache와 Bridge FDB 정보를 입력해주고, vxlan 기반의 UDP encapsulation과 터널링을 통하여 가상디바이스의 L2정보를 목적지 노드로 전송하여 통신이 되는 것을 확인하였습니다.
이에 대한 내용을 바탕으로 가상네트워크를 추가하고 통신할 때 커널 이벤트(NETLINK)를 캐치하여 동적으로 arp, fdb 갱신처리하여 컨테이너 간에 통신이 가능하도록 구성해 봅니다.
Make container without_docker_6-overlay-network_1 Sam Kim
분산환경에서 컨테이너 간의 통신은 어떻게 이루어 지는 것일까요? 3,4편에서는 호스트 안에 가상네트워크를 만들어보았습니다. 6편에서는 이를 바탕으로 분산환경에서 호스트 간에 가상 네트워크로 통신이 가능하도록 만들어 봅니다. 이 방법은 실제 쿠버네티스 flannel 등의 CNI에서 사용하고 있는 vxlan 기반의 오버레이 네트워크 구성을 다룹니다.
[Open Infrastructure & Cloud Native Days Korea 2019]
커뮤니티 버전의 OpenStack 과 Ceph를 활용하여 대고객서비스를 구축한 사례를 공유합니다. 유연성을 확보한 기업용 클라우드 서비스 구축 사례와 높은 수준의 보안을 요구하는 거래소 서비스를 구축, 운영한 사례를 소개합니다. 또한 이 프로젝트에 사용된 기술 스택 및 장애 해결사례와 최적화 방안을 소개합니다. 오픈스택은 역시 오픈소스컨설팅입니다.
#openstack #ceph #openinfraday #cloudnative #opensourceconsulting
NovaProva, a new generation unit test framework for C programsGreg Banks
I wrote NovaProva because I was sick of writing unit tests using the venerable but clunky CUnit library. CUnit looked easy when I started writing unit tests but I soon discovered it's limitations and ended up screaming in frustration. Meanwhile over 18 months the Cyrus IMAP server project has gone from 0 unit tests to 461, of which 277 are written in C with CUnit. So that's a big itch!
At LinkedIn we run lots of Java services on Linux boxes. Java and Linux are a perfect pair. Except when they're not; then there's fireworks. This talk describes 5 situations we encountered where Java interacted with normal Linux behavior to create stunningly sub-optimal application behavior like minutes-long GC pauses. We'll deep dive to show What Java Got Wrong, why Linux behaves the way it does, and how the two can conspire to ruin your day. Finally we'll examine actual code samples showing how we fixed or hid the problems.
Container security: seccomp, network e namespacesKiratech
Le slides hanno l'obiettivo di evidenziare le nuove features di sicurezza introdotte nell'ultima release docker sia descrivendone il funzionamento sia mostrando, attraverso alcune demo, l'eventuale impatto in ambienti di produzione. Viene fatta una comparazione, in termini di analisi del rischio, tra ambienti host utilizzanti engine inferiore a release 1.9 e nuove versioni, soffermandosi su mancanze e future implementazioni.
1,2편에서 다룬 chroot와 pivot_root를 통해서 root filesystem을 isolation하였습니다. 마운트 네임스페이스는 파일시스템 마운트를 isolation 하는 것으로 이미 pivot_root에서도 사용하였지만, mount 처리를 격리함으로써 컨테이너 내부의 파일시스템 구조를 독립적으로 유지합니다. 실제 도커 컨테이너의 이미지 tarball을 이용하여 pivot_root와 mount namespace까지 적용하여 실제 도커 방식과 유사하게 컨테이너를 기동하여 봅니다. 그리고, 컨테이너 이미지 용량/중복을 해결하기 위한 overlayFS 에 대하여 다룹니다.
https://netpple.github.io
Kernel Recipes 2019 - ftrace: Where modifying a running kernel all startedAnne Nicolas
Ftrace’s most powerful feature is the function tracer (and function graph tracer which is built from it). But to have this enabled on production systems, it had to have its overhead be negligible when disabled. As the function tracer uses gcc’s profiling mechanism, which adds a call to “mcount” (or more recently fentry, don’t worry if you don’t know what this is, it will all be explained) at the start of almost all functions, it had to do something about the overhead that causes. The solution was to turn those calls into “nops” (an instruction that the CPU simply ignores). But this was no easy feat. It took a lot to come up with a solution (and also turning a few network cards into bricks). This talk will explain the history of how ftrace came about implementing the function tracer, and brought with it the possibility of static branches and soon static calls!
Steven Rostedt
Kernel Recipes 2019 - Analyzing changes to the binary interface exposed by th...Anne Nicolas
Operating system distributors often face challenges that are somewhat different from that of upstream kernel developers. For instance, some kernel updates often need to stay at least binary compatible with modules that might be “out of tree” for some time.
In that context, being able to automatically detect and analyze changes to the binary interface exposed by the kernel to its module does have some noticeable value.
The Libabigail framework is capable of analyzing ELF binaries along with their accompanying debug info in the DWARF format, detect and report changes in types, functions, variables and ELF symbols. It has historically supported that for user space shared libraries and application so we worked to make it understand the Linux kernel
binaries.
In this presentation, we are going to present the current support of ABI analysis for Linux Kernel binaries, the challenges we face, how we address them and the plans we have for the future.
Dodji Seketeli, Jessica Yu, Matthias Männich
Slides of my talk on Devel::NYTProf and optimizing perl code at YAPC::NA in June 2014. It covers use of NYTProf and outlines a multi-phase approach to optimizing your perl code.
A video of the talk and questions is available at https://www.youtube.com/watch?v=T7EK6RZAnEA&list=UU7y4qaRSb5w2O8cCHOsKZDw
Lecture 2: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 1: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
At LinkedIn we run lots of Java services on Linux boxes. Java and Linux are a perfect pair. Except when they're not; then there's fireworks. This talk describes 5 situations we encountered where Java interacted with normal Linux behavior to create stunningly sub-optimal application behavior like minutes-long GC pauses. We'll deep dive to show What Java Got Wrong, why Linux behaves the way it does, and how the two can conspire to ruin your day. Finally we'll examine actual code samples showing how we fixed or hid the problems.
Container security: seccomp, network e namespacesKiratech
Le slides hanno l'obiettivo di evidenziare le nuove features di sicurezza introdotte nell'ultima release docker sia descrivendone il funzionamento sia mostrando, attraverso alcune demo, l'eventuale impatto in ambienti di produzione. Viene fatta una comparazione, in termini di analisi del rischio, tra ambienti host utilizzanti engine inferiore a release 1.9 e nuove versioni, soffermandosi su mancanze e future implementazioni.
1,2편에서 다룬 chroot와 pivot_root를 통해서 root filesystem을 isolation하였습니다. 마운트 네임스페이스는 파일시스템 마운트를 isolation 하는 것으로 이미 pivot_root에서도 사용하였지만, mount 처리를 격리함으로써 컨테이너 내부의 파일시스템 구조를 독립적으로 유지합니다. 실제 도커 컨테이너의 이미지 tarball을 이용하여 pivot_root와 mount namespace까지 적용하여 실제 도커 방식과 유사하게 컨테이너를 기동하여 봅니다. 그리고, 컨테이너 이미지 용량/중복을 해결하기 위한 overlayFS 에 대하여 다룹니다.
https://netpple.github.io
Kernel Recipes 2019 - ftrace: Where modifying a running kernel all startedAnne Nicolas
Ftrace’s most powerful feature is the function tracer (and function graph tracer which is built from it). But to have this enabled on production systems, it had to have its overhead be negligible when disabled. As the function tracer uses gcc’s profiling mechanism, which adds a call to “mcount” (or more recently fentry, don’t worry if you don’t know what this is, it will all be explained) at the start of almost all functions, it had to do something about the overhead that causes. The solution was to turn those calls into “nops” (an instruction that the CPU simply ignores). But this was no easy feat. It took a lot to come up with a solution (and also turning a few network cards into bricks). This talk will explain the history of how ftrace came about implementing the function tracer, and brought with it the possibility of static branches and soon static calls!
Steven Rostedt
Kernel Recipes 2019 - Analyzing changes to the binary interface exposed by th...Anne Nicolas
Operating system distributors often face challenges that are somewhat different from that of upstream kernel developers. For instance, some kernel updates often need to stay at least binary compatible with modules that might be “out of tree” for some time.
In that context, being able to automatically detect and analyze changes to the binary interface exposed by the kernel to its module does have some noticeable value.
The Libabigail framework is capable of analyzing ELF binaries along with their accompanying debug info in the DWARF format, detect and report changes in types, functions, variables and ELF symbols. It has historically supported that for user space shared libraries and application so we worked to make it understand the Linux kernel
binaries.
In this presentation, we are going to present the current support of ABI analysis for Linux Kernel binaries, the challenges we face, how we address them and the plans we have for the future.
Dodji Seketeli, Jessica Yu, Matthias Männich
Slides of my talk on Devel::NYTProf and optimizing perl code at YAPC::NA in June 2014. It covers use of NYTProf and outlines a multi-phase approach to optimizing your perl code.
A video of the talk and questions is available at https://www.youtube.com/watch?v=T7EK6RZAnEA&list=UU7y4qaRSb5w2O8cCHOsKZDw
Lecture 2: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 1: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 4: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 6: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 3: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 5: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Lecture 8: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
This is a series of slides prepared by Heather Kulik (http://www.stanford.edu/~hkulik or email hkulik at stanford dot edu) for a talk given at the University of Pennsylvania in February 2012. It covers a basic introduction to DFT+U and related approaches for improving descriptions of transition metals and other systems with localized electrons.
A presentation looking at the parallelisation of the Vienna ab initio Simulation Package (VASP) code, how to optimise performance and scaling by tuning the input control tags, and some initial experience with the NVIDIA GPU (CUDA) port of the code, including compiling, running jobs, and some initial benchmark results.
Some "accumulated wisdom" from several years of using the Vienna ab initio Simulation Package (VASP) code for computational modelling. Includes tips on convergence and parallelisation.
Troubleshooting common oslo.messaging and RabbitMQ issuesMichael Klishin
This talk focuses on troubleshooting of common oslo.messaging and RabbitMQ issues in OpenStack environments. Co-presented at the OpenStack Summit Austin in April 2016.
You have a system with an advanced programmatic tracer: do you know what to do with it? Brendan has used numerous tracers in production environments, and has published hundreds of tracing-based tools. In this talk he will share tips and know-how for creating CLI tracing tools and GUI visualizations, to solve real problems effectively. Programmatic tracing is an amazing superpower, and this talk will show you how to wield it!
Erik Skytthe - Monitoring Mesos, Docker, Containers with Zabbix | ZabConf2016Zabbix
At DBC we are running docker and other container types in a mesos/marathon cluster environment. I will demonstrate how we collect statistics, logs etc. and monitor this environment, showing configuration examples, data flows and templates.
Some of the covered topics:
- Mesos master and agents
- Marathon Framework
- Docker engine
- Containers
- Zookeeper
- Elasticserach/ELK
Testing Persistent Storage Performance in Kubernetes with SherlockScyllaDB
Getting to understand your Kubernetes storage capabilities is important in order to run a proper cluster in production. In this session I will demonstrate how to use Sherlock, an open source platform written to test persistent NVMe/TCP storage in Kubernetes, either via synthetic workload or via variety of databases, all easily done and summarized to give you an estimate of what your IOPS, Latency and Throughput your storage can provide to the Kubernetes cluster.
Video: https://www.youtube.com/watch?v=uibLwoVKjec . Talk by Brendan Gregg for Sysdig CCWFS 2016. Abstract:
"You have a system with an advanced programmatic tracer: do you know what to do with it? Brendan has used numerous tracers in production environments, and has published hundreds of tracing-based tools. In this talk he will share tips and know-how for creating CLI tracing tools and GUI visualizations, to solve real problems effectively. Programmatic tracing is an amazing superpower, and this talk will show you how to wield it!"
Presentació a càrrec d'Ismael Fernández i Cristian
Gomollón (tècnics d'Aplicacions al CSUC) duta a terme a la jornada de formació "Com usar el servei de càlcul del CSUC" celebrada el 8 d'octubre de 2019 al CSUC.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
2. MIT
10.637
Lecture 7
Lab 2 overview
water models:
TIP3P, TIP4P, TIP4P-FB, SPC/Fw
equilibration, production, and analysis
MgCl2 solution:
Choose one water model, add ions,
equilibrate, production, and analysis
Ubiquitin WT protein:
Get PDB file, prepare, solvate protein,
equilibrate, production, analysis
Ubiquitin mutant:
Mutate WT protein, solvate, equilibrate,
production, analysis
3. MIT
10.637
Lecture 7
AMBER nuts and bolts
AMBER dat files + Online repository:
force field files, prepin files, to describe
proteins, nucleotides, water, and ions.
antechamber/RED server:
generates force field and prepin files for
non-standard ligands and residues
tleap: organize and load in force field
properties, solvate, set box dimensions,
neutralize, and generate
topology/coordinate files
sander: run minimizations and molecular
dynamics using topology, coordinates, and
input parameters.
cpptraj/ptraj: process and analyze output
of trajectories.
4. MIT
10.637
Lecture 7
Using XSEDE
For those who didn’t set up aliases last time:
1) Login to the XSEDE login portal
ssh <xsede username>@login.xsede.org
2) Login to the Maverick machine
gsissh -p 2222 maverick.tacc.xsede.org
Once on Maverick, copy files as needed over from your athena machine:
scp <Athenausername>@athena.dialup.mit.edu:~/<local file name> ./
We’ll want to add a few commands to your bashrc. These are:
export AMBERHOME=/work/02958/hkulik/maverick/shared/amber/
export
LD_LIBRARY_PATH=/work/02958/hkulik/maverick/shared/amber/lib:$LD_LIB
RARY_PATH
export PATH=/work/02958/hkulik/maverick/shared/amber/bin:$PATH
You can add them by editing your ~/.bashrc:
nano ~/.bashrc
Then:
source ~/.bashrc
5. MIT
10.637
Lecture 7
tleap
Tleap takes commands or an input file.
Example input commands:
source leaprc.ff14SB
mol = loadpdb wat.pdb
check mol
solvatebox mol TIP3PBOX 14.37
savepdb mol tip3pwaterbox.pdb
saveamberparm mol tip3pwater.prmtop tip3pwater.inpcrd
quit
6. MIT
10.637
Lecture 7
Maverick SLURM queue
• Maverick uses SLURM as a queueing system.
• We write a job script and then submit it to the queueing system to run when
resources are available.
• Example job script:
#!/bin/bash
#SBATCH –J equilibration
#SBATCH –o equil.oe
#SBATCH –N 1
#SBATCH –p gpu
#SBATCH –t 12:00:00
#SBATCH –n 1
. /usr/local/etc/login
module load cuda/6.0
module load intel
#Example run command
./exec < input > output
7. MIT
10.637
Lecture 7
Maverick SLURM queue
• We issue commands to the SLURM queue to manage our jobs.
• Submit the job script:
sbatch <jobscript>
• Submit a job that depends on another one:
sbatch –d <slurm job #> <jobscript>
• Check the status of all of your jobs
showq –u <xsede username>
• Check the status of everyone’s jobs
showq
• Check specifics of a running or queued job
scontrol show job <slurm job #>
• Cancel a job
scancel <slurm job #>
8. MIT
10.637
Lecture 7
sander
Minimization example:
unrestrained_min.in:
&cntrl ! Control namelist
imin = 1, ! Minimization is on
maxcyc = 2000, ! Number of cycles to run minimization
ncyc = 2000, ! Number of cycles to run steepest descent
ntb = 1, ! Constant volume PBCs
cut = 9.0, ! Nonbonded cutoff distance in Angstroms-this
is a little small, but our simulation cell is a bit small.
ntxo = 2, ! NetCDF file for coordinates and restart
ioutfm = 1, ! Binary NetCDF trajectory
/
9. MIT
10.637
Lecture 7
sander
Dynamics example:
constV_equil.in:
&cntrl !Control namelist
nstlim=5000, !Number of dynamics steps
dt=0.002, !Timestep in ps**
ntx=1, !Read in the coordinates without velocities.
irest=0, !We are not restarting the simulation
ntpr=500, !How frequently we print progress
ntwr=5000, !How frequently we write the restart file
ntwx=5000, !How frequently we write the mdcrd file
tempi=100.0, !Initial temperature
temp0=298.15, !Reference target temperature- to compare to
experiment
ntt=3, !Weak coupling thermostat
gamma_ln=1.0, ! Time constant in ps for heat bath coupling.
ig=-1, !Random seed for starting velocities.
ntb=1, ! Constant volume PBCs
ntc=2, ! SHAKE algorithm to constrain bonds with hydrogen**
ntf=2, ! Interactions involving H-atoms omitted**
cut = 9.0, ! Nonbonded cutoff distance in Angstroms
ntxo=2, ! NetCDF file for coordinates and restart
ioutfm=1, ! Binary NetCDF trajectory
/
10. MIT
10.637
Lecture 7
cpptraj/ptraj
cpptraj processes our trajectory files. It takes an input file, command line
options, or work at the interactive prompt.
To start, we specify a prmtop file:
$AMBERHOME/bin/cpptraj –p <myprmtop>
Example queries:
trajin <mdcrd file>
(can take multiple mdcrd files and will sequentially load them)
trajout mdcrd.pdb pdb
radial myrdf.rdf 0.05 15.0 @O density 0.0033
distance mgcl @MG :2@CL- out mg-cl.dist
go
quit
11. MIT
10.637
Lecture 7
Working with athena
• Make sure terminal is locked to launcher.
• Pick a text editor to use and get
comfortable– nano for most of you.
• Try some basic linux commands.
12. MIT
10.637
Lecture 7
Logging into athena
• Locally: here in 14-0637
• Quick stations on campus
• Athena clusters (eg bldg 56)
– At commandline: tellme combo
• Remotely: X11 programs (eg avogadro)
will be very slow over ssh but may be
possible with fast internet at MIT.
– ssh –X <athena
username>@athena.dialup.mit.edu
13. MIT
10.637
Lecture 7
Commandline tips
ls: lists all visible files in the current directory.
Try: ls -ltrh
to view files with long printing (l), last modified sorting (t),
in reverse (r), and human readable (h) file sizes.
Try: ls .*
to view all hidden files that start with ‘.’ such as .bashrc.
Try: ls */*
to view all files in first layer of subdirectories, etc.
Try: ls */ -d
to view all files that match a wildcard with a directory.
14. MIT
10.637
Lecture 7
Commandline tips
cd: change directory.
Try: cd ~/
to change directory to home
Try: cd -
to change directory to the previous one.
Try: cd ../
to move up one directory
15. MIT
10.637
Lecture 7
Commandline tips
mkdir: make a directory.
Try: mkdir -p path/to/directory
to simulatenously make new directory path, with a subdirectory
inside to, with sub-subdirectory inside called ‘directory’
pwd: gets the current working directory.
ln: make a symbolic link for a directory.
Say you have a long source directory like
/usr/local/source/file/compiler/bin/ and want to be able to see its
contents more easily.
Try: ln -s /usr/local/source/file/compiler/bin/ easydir
to make a symbolic link in your existing directory as a
subdirectory called “easydir”.
16. MIT
10.637
Lecture 7
Commandline tips
cp/mv: copy or move files from one place to another. You may want to copy or
move files around from one place to another. Here are some examples of
copying or moving the old file apples.txt to oranges.txt.
Try: cp -i apples.txt oranges.txt
“i” for interactive means that if oranges.txt already exists, it will ask you if you
want to overwrite.
Try: mv -i apples.txt oranges.txt
“i” for interactive means that if oranges.txt already exists, it will ask you if you
want to overwrite the existing oranges.txt.
Try: mv -f apples.txt oranges.txt
“f” forces the move even if an existing oranges.txt is already there.
Try: cp -p apples.txt oranges.txt
“p” means that permissions and timestamps will be preserved.
Try: cp -r apples/ oranges/
“r” means that you’re recursively copying all the files in a directory. You need to
do this if you’re trying to copy a directory.
17. MIT
10.637
Lecture 7
Commandline tips
rm: remove a file.
Much like cp and mv, you can remove files (be
careful with this) using a couple different flags.
Try: rm -i apples.txt
to interactively ”i” remove a file (i.e. get a y/n
statement)
Try: rm -v apples.txt
to get a verbose listing of the files removed.
Try: rm -r apples/
to recursively remove an entire directory.
18. MIT
10.637
Lecture 7
Logging into XSEDE machines
• Best way:
– ssh <xsede portal username>@login.xsede.org
– enter your portal username password
– also, you can add an alias:
• In athena, probably using cshell:
– nano ~/.cshrc.mine
– alias xsede 'ssh <username>@login.xsede.org'
• In bash:
– nano ~/.bashrc
– (on a mac) nano ~/.profile
– alias xsede=‘ssh <username>@login.xsede.org’
– Once at the portal, commands for passwordless login to other machines show up in
MOTD:
• Trestles: gsissh trestles.sdsc.xsede.org
• Maverick: gsissh -p 2222 maverick.tacc.xsede.org
• Alternatives:
– You may be able to login to these machines directly (YMMV)
• ssh <portalusername>@maverick.tacc.xsede.org (likely works)
• ssh <portalusername>@trestles.sdsc.xsede.org (probably doesn’t work)
19. MIT
10.637
Lecture 7
Aliases
• Useful way to associate long linux commands
with shortcuts
• Forgot which aliases you have set? Type
alias at the commandline
• If you set aliases, you will need to reinitialize
the shell before they’re active. E.g. in bash
type ‘bash’ in cshell type ‘tcsh’ or log out and
log in again.
20. MIT
10.637
Lecture 7
Copying data
To access data from other machines, use secure copy. You may want to do this
to an open machine such as an athena machine:
Syntax from remote machine to current location:
scp <remote username>@<remote machine>:<remote file loc> <local loc>
Syntax from local machine to remote machine:
scp <local loc> <remote username>@<remote machine>:<remote dir>
You can do this by copying from Maverick/Trestles->Xsede Login->Home
machine
Or you can copy from Maverick/Trestles->Athena.
21. MIT
10.637
Lecture 7
Summary
• Review on your own, more commandline tips:
– http://hjklol.mit.edu/content/bios-203-useful-
commandline-tools
– Or check for cheat sheet on Stellar.
• Make sure you have set up your xsede
account before you leave today!
• Let’s get started next time with molecular
mechanics!
• Any questions?